Brown stem rot (BSR) is a major disease of soybean (Glycine max) that is prevalent in the soybean-growing regions of the northern United States (U.S.) and in Canada (Klos, et al., Crop Sci 40:1445-1452 (2000)). The causative agent, Phialophora gregata, is a soil-borne fungus which can induce browning of internal stem and root tissue and can cause premature leaf abscission in susceptible plants. A major effect of P. gregata infection is loss of yield which has been estimated to exceed 20 million bushels a year in the north central U.S. (Doupnik B., Plant Disease, 77: 1170-1171 (1993)). Two strains of P. gregata have been identified, both of which are associated with yield loss in soybean. The defoliating Type I strain results in more severe symptoms than the non-defoliating Type II strain (Hughs, et al., Plant Disease 86:729-735 (2002)). P. gregata enters soybean plants through the roots and then infects pith and vascular tissue. The pathogen does not produce long-term survival structures; however, it can reproduce in soybean residue remaining in a field. Subsequent soybean crops planted in fields harboring such infected soybean residue may develop BSR.
Methods to control BSR include crop rotation and planting BSR resistant soybean varieties. Three quantitative trait loci, Rbs1, Rbs2 and Rbs3, have been described which are associated with BSR resistance in soybean. Rbs1 was described in soybean variety L78-4094 (Hanson, et al., Crop Sci 28:41-43 (1988)), Rbs2 in PI 437833 (Hanson, et al., Crop Sci 28:41-43 (1988)), and Rbs3 in PI 437970 (Willmot and Nickell, Crop Sci 29:672-674 (1989)). All three resistance loci are located on Linkage Group J (LG J) of the soybean genetic linkage map (Cregan, et al., Crop Sci 39:1464-1490 (1999); Bachman et al., Crop Sci 41:527-535 (2001); Patzoldt, et al., Crop Sci 45:1092-1095 (2005)).
Selection for BSR resistant plants based on phenotypic screening is labor-intensive and time consuming. The use of molecular markers in a soybean breeding program can greatly increase the efficiency of selection for and introgression of BSR resistance in plants. Marker analysis has identified simple sequence repeat (SSR) markers such as SATT244 linked to Rbs loci (Bachman et al., Crop Sci 41:527-535 (2001)). Molecular markers have been used in soybean breeding to detect, and select for, BSR resistance loci. In the case of BSR susceptible plants, molecular markers can be used to introgress BSR resistance from BSR resistant sources. Restriction fragment length polymorphisms (RFLPs) have been provided for BSR resistant locus Rbs3 (U.S. Pat. No. 5,689,035 and U.S. Pat. No. 5,948,953). In addition, SSRs, expressed sequence tags (ESTs), and RFLPs have been provided for Rbs1, Rbs2, and Rbs3 (U.S. Patent Application Publication Number 2006/0041955).
Of the classes of markers, single nucleotide polymorphisms (SNPs) have characteristics which make them preferential to other genetic markers in detecting, selecting for, and introgressing BSR resistance in a soybean plant. SNPs occur in plant populations as a result of single nucleotide substitutions or insertion/deletion (INDEL) events in the genomes of individual plants. SNPs are preferred because technologies are available for automated, high-throughput screening of SNP markers, which can decrease the time and resources needed to select for and introgress BSR resistance in soybean plants. Further, SNP markers are ideal because the likelihood that a particular SNP allele is derived from independent origins in the extant population of a particular species is very low. As such, SNP markers are useful for tracking and assisting introgression of BSR resistance alleles, particularly in the case of BSR resistance haplotypes. A need exists for a SNP based marker set to screen for resistance to BSR. The present invention provides a SNP-based marker set for Rbs1, Rbs2, and Rbs3 on Linkage Group J. As used herein, the term “Rbs” includes Rbs1, Rbs2, and Rbs3.
The present invention provides and includes methods and compositions for screening and selecting a soybean plant comprising QTL for BSR resistance that were derived from mapping populations using endemic strains of Phialophora gregata and single nucleotide polymorphisms (SNP) marker technology.